Structure of PDB 5gwk Chain B Binding Site BS05

Receptor Information
>5gwk Chain B (length=724) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KGIPKLDDANDAGGRNSTECTLILTEGDSAKTLAVSGLGVVGRDKYGVFP
LRGKILNVREASHKQIMENAEINNIIKIVGLQYKKNYEDEDSLKTLRYGK
IMIMTDQDQDGSHIKGLLINFIHHNWPSLLRHRFLEEFITPIVKVSKNKQ
EMAFYSLPEFEEWKSSTPNHKKWKVKYYKGLGTSTSKEAKEYFADMKRHR
IQFKYSGPEDDAAISLAFSKKQIDDRKEWLTNFMEDRRQRKLLGLPEDYL
YGQTTTYLTYNDFINKELILFSNSDNERSIPSMVDGLKPGQRKVLFTCFK
RNDKREVKVAQLAGSVAEMSSYHHGEMSLMMTIINLAQNFVGSNNLNLLQ
PIGQFGTRLHGGKDSASPRYIFTMLSSLARLLFPPKDDHTLKFLYDDNQR
VEPEWYIPIIPMVLINGAEGIGTGWSCKIPNFDVREIVNNIRRLMDGEEP
LPMLPSYKNFKGTIEELAPNQYVISGEVAILNSTTIEISELPVRTWTQTY
KEQVLEPMLNGTPPLITDYREYHTDTTVKFVVKMTEEKLAEAERVGLHKV
FKLQTSLTCNSMVLFDHVGCLKKYDTVLDILRDFFELRLKYYGLRKEWLL
GMLGAESAKLNNQARFILEKIDGKIIIENKPKKELIKVLIQRGYDSDPVK
AWKEAQQSGPTFNYLLDMPLWYLTKEKKDELCRLRNEKEQELDTLKRKSP
SDLWKEDLATFIEELEAVEAKEKQ
Ligand information
Ligand IDEVP
InChIInChI=1S/C29H32O13/c1-11-36-9-20-27(40-11)24(31)25(32)29(41-20)42-26-14-7-17-16(38-10-39-17)6-13(14)21(22-15(26)8-37-28(22)33)12-4-18(34-2)23(30)19(5-12)35-3/h4-7,11,15,20-22,24-27,29-32H,8-10H2,1-3H3/t11-,15+,20-,21-,22+,24-,25-,26-,27-,29+/m1/s1
InChIKeyVJJPUSNTGOMMGY-MRVIYFEKSA-N
SMILES
SoftwareSMILES
CACTVS 3.370COc1cc(cc(OC)c1O)[C@H]2[C@@H]3[C@H](COC3=O)[C@H](O[C@@H]4O[C@@H]5CO[C@@H](C)O[C@H]5[C@H](O)[C@H]4O)c6cc7OCOc7cc26
OpenEye OEToolkits 1.7.2CC1OCC2C(O1)C(C(C(O2)OC3c4cc5c(cc4C(C6C3COC6=O)c7cc(c(c(c7)OC)O)OC)OCO5)O)O
OpenEye OEToolkits 1.7.2C[C@@H]1OC[C@@H]2[C@@H](O1)[C@@H]([C@H]([C@@H](O2)O[C@@H]3c4cc5c(cc4[C@H]([C@@H]6[C@@H]3COC6=O)c7cc(c(c(c7)OC)O)OC)OCO5)O)O
ACDLabs 12.01O=C1OCC7C1C(c2cc(OC)c(O)c(OC)c2)c4cc3OCOc3cc4C7OC6OC5C(OC(OC5)C)C(O)C6O
CACTVS 3.370COc1cc(cc(OC)c1O)[CH]2[CH]3[CH](COC3=O)[CH](O[CH]4O[CH]5CO[CH](C)O[CH]5[CH](O)[CH]4O)c6cc7OCOc7cc26
FormulaC29 H32 O13
Name(5S,5aR,8aR,9R)-9-(4-hydroxy-3,5-dimethoxyphenyl)-8-oxo-5,5a,6,8,8a,9-hexahydrofuro[3',4':6,7]naphtho[2,3-d][1,3]dioxol -5-yl 4,6-O-[(1R)-ethylidene]-beta-D-glucopyranoside;
Etoposide;
VP-16
ChEMBLCHEMBL44657
DrugBankDB00773
ZINCZINC000003938684
PDB chain5gwk Chain D Residue 102 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5gwk Producing irreversible topoisomerase II-mediated DNA breaks by site-specific Pt(II)-methionine coordination chemistry
Resolution3.152 Å
Binding residue
(original residue number in PDB)
G462 D463 R487 M766
Binding residue
(residue number reindexed from 1)
G27 D28 R52 M331
Annotation score1
Binding affinityBindingDB: EC50=810nM,IC50=56000nM
Enzymatic activity
Enzyme Commision number 5.6.2.2: DNA topoisomerase (ATP-hydrolyzing).
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003918 DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity
GO:0005524 ATP binding
Biological Process
GO:0006259 DNA metabolic process
GO:0006265 DNA topological change

View graph for
Molecular Function

View graph for
Biological Process
External links
PDB RCSB:5gwk, PDBe:5gwk, PDBj:5gwk
PDBsum5gwk
PubMed28977631
UniProtP11388|TOP2A_HUMAN DNA topoisomerase 2-alpha (Gene Name=TOP2A)

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